☰ Navigation Tabs
Crystal structure of monkey TLR7 in complex with loxoribine and polyU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 3350, magnesium chloride, sodium citrate pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.84 56.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.277 α = 90 b = 99.41 β = 98.58 c = 112.096 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2015-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.59 50.01 93.9 0.08 15.1 2.8 58705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 0.41
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5GMF 2.6 50.01 58494 3088 93.55 0.21719 0.21502 0.2161 0.25833 0.2608 RANDOM 67.759
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.41 2.59 3.04 -3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.648 r_dihedral_angle_4_deg 20.86 r_dihedral_angle_3_deg 16.374 r_long_range_B_refined 10.755 r_long_range_B_other 10.753 r_scangle_other 8.249 r_mcangle_it 7.438 r_mcangle_other 7.437 r_dihedral_angle_1_deg 6.939 r_scbond_it 5.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.648 r_dihedral_angle_4_deg 20.86 r_dihedral_angle_3_deg 16.374 r_long_range_B_refined 10.755 r_long_range_B_other 10.753 r_scangle_other 8.249 r_mcangle_it 7.438 r_mcangle_other 7.437 r_dihedral_angle_1_deg 6.939 r_scbond_it 5.387 r_scbond_other 5.383 r_mcbond_it 5.05 r_mcbond_other 5.05 r_angle_refined_deg 1.666 r_angle_other_deg 1.13 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12326 Nucleic Acid Atoms 128 Solvent Atoms 33 Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing